Research Projects

Shannon develops and utilizes molecular resources to study and manage vernal pool branchiopods. These resources include qPCR-based eDNA and metabarcoding tools, a large, multi-species RAD-sequencing study, and three new reference-quality genomes.

High Quality Genomic Resources for Vernal Pool Branchiopods

As a postdoc, Shannon is sequencing and assembling fully-scaffolded, reference-quality genomes for the vernal pool branchiopods Branchinecta lynchi (Threatened), Branchinecta lindahli, and Lepidurus packardi (Endangered). This projects is funded by the U.S. Bureau of Reclamation, and resources will be published open-access in the Journal of Heredity through a collaboration with the California Conservation Genomics Project. These genomes can be used to study the adaptation and divergence of these species, in addition to answering questions about sex determination and genomic architecture.

Using RAD-Seq to Understand the Population Genetics of Vernal Pool Crustaceans

Shannon traveled across California and Oregon to collect more than 1000 vernal pool crustaceans representing more than 25 sampling sites across 12 counties, covering five species. These samples were sequenced using RAD-seq protocols to comparatively describe their population genetics in a report for U.S. Fish and Wildlife in collaboration with the U.S. Bureau of Reclamation and in her dissertation. For one species, she dove deeper into their evolutionary history, genetic isolation, migration rates and connectivity to better understand how dispersal vector loss and habitat fragmentation may be affecting this threatened vernal pool community member. This work will be published in a forthcoming peer-reviewed publication. RAD-sequencing is a popular tool developed in part by Animal Science professor and collaborator Dr. Michael Miller which can provide SNP-based genetic information at thousands of loci without the need for a reference genome.

Environmental DNA Resources to Monitor and Manage Vernal Pool Species in California

Shannon is using non-invasive environmental DNA (eDNA) techniques to study vernal pool branchiopods. She is collecting water samples from vernal pool complexes in Sacramento and Merced counties in order to examine genetic diversity using both targeted assays for four crustacean species and the protected California Tiger Salamander. She is also using metabarcoding techniques to answer questions about vernal pool community makeup across California. eDNA is an emerging field of research that examines trace genetic material left in the environment, such as water, feces or soil.